Computational Biophysics & Bioinformatics - Dr. Emil Alexov Group

Delphi Force is a DelPhi-based script, allowing to calculate the
electrostatic force between two objects, such as proteins, DNAs, lipids, small molecules, etc.

The calculation only requires two PQR files of the two objects. These file
can be generated by our DelPhipKa
webserver.

This server outputs the forces on each individual residue, and generates
pictures to visualize the forces using arrows. In the pictures, the blue arrow shows the total force,
the red arrows show the forces on individual residues. The server also provides VMD TCL scripts for the
users to make their own pictures.

Structure of Calmodulin in calcium loaded and peptide free state
(PDB: 5E1K). N-terminal
lobe, C-terminal lobe and calcium ions are colored as grey, cyan and orange. The total
electrostatic force is shown as blue arrow and the forces applied on each residue are
represented as red arrow (The size of the arrows are adjusted for the best visualization).

Structure of p53 core domain in complex with DNA (PDB: 4HJIE). The
p53 core domain binds to DNA as a cooperative tetramer and each monomer is shown as different
color. The p53 core domains were moved 20 Å away from DNA along the mass center. The total
electrostatic force is shown as blue arrow and the forces applied on each residue are
represented as red arrow (The size of the arrows are adjusted for the best visualization).

DelPhi Force calculates the forces of atoms/residues on the "target" molecule under
the electrostatic field generated by the "reference" molecule. For more detailed
instructions, please check our paper and
tutorial.

To calculate forces between two residues or a group of residues in a "reference"
structure, use the Residues(s) Pairwise Interaction mode.

Standard PQR format contains the following information for each atom: index, name,
residue name, 3D coordinates, charge, radius. You can generate a PQR file using a
PDB file and our
DelPhipKawebserver.
This will allow you to create a PQR at desired pH.

DelPhi Force calculates the forces of atoms/residues on the "target" molecule under
the electrostatic field generated by the "reference" molecule. For more detailed
instructions, please check our paper and
tutorial.

To calculate forces between two residues or a group of residues in a "reference"
structure, use the Residues(s) Pairwise Interaction mode.

Standard PQR format contains the following information for each atom: index, name,
residue name, 3D coordinates, charge, radius. You can generate a PQR file using a
PDB file and our
DelPhipKawebserver.
This will allow you to create a PQR at desired pH.